(092112)

Thermodynamics
and the Molecules of Life

Making biology's important molecules requires energy.

Questions:

Is
there something inherent in the laws and principles
of chemistry that make life's start a sure event?

Where
did the first molecules of life get this energy?

Is
there some easy way to get past the high energy
requirements associated with producing biological
molecules?

What
do we learn by making some calculations?

Does
thermodynamics get us any closer to explaining how
life got started?

Short
Answer:

Thermodynamics
101 (albeit watered down a bit!):
Simple chemicals with a bit of energy alone—absent
of biological systems—may contribute to making
a few but not all of the complex molecules required
for life. And how is energy applied in wide open
space—the great out-of-doors—on a primitive
planet? Also, if some energy flows into an area
where some chemicals have collected, does that assure
us of a start to life?

Energy requirements
are a critical barrier that must to be bridged in order for a reaction
to go forward.

A
+ B + energy = C

Without
energy A and B won't combine. That's a typical case for atoms and simple molecules
that might combine to produce biologically significant compounds.
Certainly, some of what chemistry offers includes examples of chemicals
that will spontaneously make products—even give off energy
instead of consuming energy—but these aren't the key biological
substances that count in this discussion.

Energy pushes the reaction to make product C. You can't
roll a stone down the hill until you have used energy to get to the top of
the hill in the first place! This is one way to think of thermodynamics in
simple terms. The equals sign is like getting to the top of the hill and making
the last little push ... this requires energy that once added makes production
of C look easy.

So, everyday
principles of chemistry tell us that unless the barrier is surpassed,
life's molecular building blocks would be rare to nonexistent on
a primitive planet. Not to mention that one would need to put all
the required chemical products in just the right place—and
in sufficient quantities—to make a plausible scenario. And
the expansive land and water surface of the planet might cause
diffusion rather than concentrating key components. Even with some
spontaneous reactions that might be assisted by energy from heat,
lightening, or other naturally occurring source, the total package—in
thermodynamic terms—still needs to be assembled. Something
or someone has to put all the ingredients in one place to make
the first cell. Where did that help come from? So maybe, at best,
all this describes a low probability proposition.

The short
answer tells us that the principle of thermodynamics is a potential
show stopper. Even if basic ingredients are present, the energy
requirements pose a significant hurdle. Further, there is a complexity
to putting together molecules such that life will work properly.
So, energy plus information need to be actively coupled somehow.
And there seems no scenario to explain this in a simple physical
system such as the primitive earth. In fact, there is no such evidence
for spontaneous assembly of these molecules on the planet today.
Remember, in the previous discussion it appears that the primitive
conditions may be sufficiently similar to today's. If molecules
and life itself had an inherent spontaneous property of self-assembly,
then we'd find clues to this even now. But without the clues we
are left with a mystery—and thermodynamics helps to provide
reasons why life's appearance cannot be readily explained by science
alone. Why don't more people just know this is true? Again, so
much is assumed. We get the "standard
story" in place of this information and thus to avoid
the simple truth of the matter in question!

Consider
This :

In
simplest terms, the laws of thermodynamics tell
us something about how chemistry—and even the
universe—works. From the perspective of making
biological compounds, one cannot merely dump simple
chemicals into a bowl and expect complex products.
There needs to be some form of help to make reactions
go forward.

Applying
energy does the trick. But biological systems use
enzymes and cofactors to reduce the energy requirements,
to speed up reactions, that otherwise would take
forever or never happen spontaneously. That is,
energy free in the environment might come from heat,
lightening, static electricity, or light, but there
is still an element of randomness to the application
of these sources. To coordinate a real production
of significant amounts of chemical compounds requires
a directed flow of information and energy.

The
key concept is that biological function
is integrally connected to highly specific
arrangements of the molecular building
blocks in the biopolymers. It has been
demonstrated that this molecular complexity
can be quantified using information theory.
Thus the enigma of the origin of life
can ultimately be reduced to a question
whether information-intensive molecules
can be produced from simple building
blocks with only the flow of energy through
the system and, possibly, the intervention
of molecular selection of some sort. Bradley and Thaxton (CH) Page 179

The previous consideration
of chemical origins reveals
how the primitive earth was not conducive to either forming or maintaining
the products of chemical reactions in a presumed primordial soup. Even laboratory
conditions where a scientist controls conditions to favor chemical reactions—such
as those initiated by Miller and Urey—yields limited results. And the
more complex chemistry of life is also found to be difficult to reproduce
under the best of laboratory conditions. Bradley
and Thaxton (CH,
Page 182) note how
Robert Shapiro, a Harvard-educated DNA chemist from New York University, revealed (in discussion at a 1986 meeting of the International Society for the Study of the Origin of Life (ISSOL) meeting
in Berkeley) that prebiotic conditions are not favorable (i.e., impossible)
for production of the all important ribose sugar. This is a molecule critical to life function. Is this the only such example of a key molecule that's difficult
to synthesize?

... Dose, who includes
ribose, deoxyribose and replicable oligo or polynucleotides in his
list of hard-to- synthesize molecular building blocks. Horgan also
notes that RNA and its building blocks are difficult to synthesize
in a laboratory under the best of conditions, much less under plausible
prebiotic ones. Bradley
and Thaxton (CH) Page 182

Again,
thermodynamics dictates that an energy requirement must be met
before any chemical reaction can come about. So, even under the
guidance of human intelligence there is no spontaneous appearance
of chemical components that then fall into place leading to a functioning
precursor of biological life. Certainly there is much intrigue
and wonder that can be ascribed to the chemical roots that must
have grown into life's appearance. But we are face with the chicken
or the egg dilemma. Without macromolecules that are necessary components
of any living cell one cannot have a functioning cell. But how
did these form and how did they first get to a place that allowed
them to compose the cell in the first place. More than simple free
energy is required. On the other hand, given the mastery of cellular
systems—coordinated by complex information—the manufacturing
of complex biomolecules is facilitated by enzymes and cofactors
that reduce all thermodynamic barriers and allow rapid production
of every molecule needed—even those that are hard to make
in a laboratory under the best of conditions.

The
cell performs thousands of different
chemical reactions. Each reaction consists
of changing a molecule into one or more
others. All the chemical reactions in
a cell are mediated by catalysts.
A catalyst always comes out of a reaction
unchanged, and it can be reused indefinitely. Spetner
(NBC) Page 31

No matter how life achieved
its biochemical mastery of cellular chemistry, there is a remarkable trick
in all this. As in the simple example at the top of this page, once energy
is used to "operate" a reaction, it is consumed and tied up in the
product. Energy use is a one shot option. But cells use enzymes as catalysts
that can be repeatedly used over and over ... and very rapidly recycle to
product several to hundreds of molecules in minutes. Now
that's really cool! Seems engineered!

Note
that enzymes are proteins that make reactions go ... and these are reactions
by any other standard, under any ordinary set of conditions, that would
go nowhere. This is a tailor made process with a specific enzyme engineered
especially for a specific reaction!

And enzymes speed up a reaction rate
by a factor of at least a million [Darnell
et al. 1986]. An increase in rate by
factors of ten billion to a hundred trillion
are not uncommon [Kraut 1988]. A factor
of a hundred trillion means that what
takes a thousandth of a second with the
enzyme would take about 3000 years without
it. Most biochemical reactions would
take so long without their enzyme that,
in effect, they wouldn't go at all. Because
enzymes controlled nearly all chemical
reactions in the cell, we can say that,
to a large extent, proteins control the
chemistry of life [Stryer 1988]. Spetner
(NBC) Page 32

The
catalysts persist whereas more and more energy would
be required if energy alone were to drive chemical
synthesis. Why didn't chance and random evolutionary
processes produce something less efficient? How
did something so well designed become the cornerstone
to cell chemistry? Yes, it might have been 'selected'
naturally, but then how did it arise in the first
place?

To
be clear, energy can be sort of a two-way street. Some reactions release energy
while others require it be added. We previously considered the composition
of the earth's early atmosphere. If Miller and Urey were correct by their
assumptions, maybe energy could be less a requirement. But if the recent evidence
is for a primitive earth wrapped in nitrogen,
carbon dioxide and water vapor, then energy would certainly be a critical
requirement ...

... making amino
acids out of ammonia, methane and hydrogen is an exothermic reaction
(energy released) with an enthalpy decrease of approximately 200 Kcal
/ mole. By contrast, making amino acids out of nitrogen, carbon dioxide
and water vapor is an endothermic reaction (energy must be added) with
an enthalpy increase of +50 Kcal / mole. Small wonder that chemists
prefer Oparin's hypothetical, but incorrect, atmosphere of ammonia,
methane in and hydrogen. Bradley and Thaxton (CH) Page 184

In a chapter on thermodynamics
and chemical origins, Bradley and Thaxton review energy requirements in relation
to the production of functional proteins and DNA. Might energy flow through
a simple system to create these complex molecules! The Natural History Museum
in Washington, D.C., features an exhibit with a video that suggests that alternating
cycles of heat and thus drying followed by wet conditions imparts energy and
potentially explains how chemicals formed on earth. Is this cycling sufficient
to explain the flow of energy through a primitive system? To be clear, the
museum exhibit can only suggest a possibility because no clear explanation
can be given. So, the analysis by Bradley and Thaxton serves to give a much
needed critical look at this topic.

The analysis sounds
a bit technical. But making the macromolecules of life (DNA, RNA and proteins)
needs energy:

...
energy flow available in the early
earth might have been suitable to make
the biopolymers of life. ...
In terms of classical thermodynamics,
polymerization will proceed spontaneously
if the Gibbs free energy (G) associated
with polymerization, or the joining
of the building blocks, decreases ([delta]G
is smaller than 0). However, if the
assembly of the building blocks results
in an increase in the Gibbs free energy
in the system ([delta]G is greater
than 0), then work is required to cause
of this chemical reaction to go forward. Bradley
and Thaxton (CH) Page 185

... Thus energy flow through the system
must be able to provide enough work to raise the system to the higher
energy level associated with the polymerized building blocks. If a
typical protein contained approximately one hundred amino acids, then
the total work required would be three hundred kilocalories per mole
of protein formed to get a "random" assembly of the amino acids. Bradley
and Thaxton (CH) Page 186

The last quotation above is part of the discussion
that looks at calculations for what is really needed to make the chemical
products for life.

Research shows that amino acids
can link to form polymers by driving off water. In such cases heat
becomes an energy flow moving through a system. This is perhaps
the source for the National Natural History Museum's video presentation
concerning chemical origins. But Bradley
and Thaxton remind us that the order or arrangement of the amino
acids is vital, ordered, and specific to a protein's function.
And as we noted previously, the L-amino acids are the biological
choice. So, a random assembly of L- and R-amino acids does not
work. Something beyond the principles of thermodynamics applies
to this selective factor.

Other
factors to consider include the type of bond formed between amino
acids:

...
the peptide bond ... represents only
one of several possible ways that amino
acids may be joined together. Analysis
of the bonds formed when the amino acids
are joined in prebiotic simulation experiments
indicate that no more than half of the
bonds are peptide bonds. Yet functional
protein requires 100 percent peptide
bonds to be able to fold into the particular
three-dimensional structures that give
biological function. Bradley
and Thaxton (CH) Page 186

Function is related
to structure and shape ... and to get the specific molecule requires energy:

The
three-dimensional topography that determines
biological function depends on the sequencing
of these amino acids. ... The additional
work required to get this degree of specificity
can be calculated to be 18.2 Cal / gm
for one hundred active sites or 9.1 cal
/ gm for fifty active sites in a protein
molecule consisting of one hundred amino
acids. Bradley
and Thaxton (CH) Page 187

In
simple terms, the bigger and more specific a protein,
the more energy is required to make this biospecific-molecule.
And remember, the larger and more complex molecules
need more information applied (somehow!) to direct
the construction of the specific molecule!

Furthermore,
once a specific molecule is produced—say in that primordial
soup—there needs to be the specific molecule that fits the
protein's enzymatic active site. There is no economy in making
a protein whose function is of no use! And this somehow has to
relate to all the other molecules that would have arisen in the
primitive chemical scenario:

... possibly the most difficult
problem in assembling amino acids into chains that fold into three-dimensional
structures that give biological function is to react the amino acids
only with each other and not with the many other chemical substances
that would be present in a prebiotic soup. The fact that one has to
do work (30 cal /gm) to chemically react amino acids with each other
indicates that amino acids do not readily react chemically. ... So it
is difficult to imagine how amino acids could be either concentrated
in solution or selectively absorbed on surfaces such as clays before
they were consumed in a chemical reactions with other substances in
the prebiotic soup. Bradley
and Thaxton (CH) Page 187

The
latter comment addresses one of the many alternative
ideas for chemical evolution—but an idea
like the rest that encounter impracticalities.
In spite of the complexities cited above, Bradley
and Thaxton made calculations for the energy
required for the random assembly of amino acids:

We
have calculated the work required to provide the necessary
specified complexity in a protein of one hundred amino acids
and found it to be similar in magnitude (18.2 + 4.2 + 4.2
cal/gm) to the required work to get our random assembly of
the building block (30 cal /gm), if we neglected the
major problem of amino acids' tendency to react with other
molecular species in the prebiotic soup. Bradley
and Thaxton (CH)
Page 188

Energy
is required and what specifically keeps
the amino acids available for only the right
reactions? So now we arrive at problems:

While energy flow
is clearly able to do the required work
to get assembly, it is doubtful that
energy flow is ever coupled to, or capable
of, the generation of information. ...
Biological information ... has no physical
connection whatsoever. Bradley
and Thaxton (CH) Page 188

These
points may sound familiar to statements made in
our prior feature article, but here we are adding
the perspective of thermodynamics as it relates to energy requirements to get the
work done. But as before we seem to run into
the issue of information and the gap between the mere physical world and
the leap into the biological framework of life itself.

Bradley and Thaxton
note that many prebiotic simulation experiments concern making proteins following
some Miller-Urey type scenario. Much of the selective process favoring production
of products like amino acids comes from the laboratory setup and the design
created by the scientist. We think this introduces an element of intelligence
and design, but even with this effort ...

The
net result is that even "contrived prebiotic"
simulation experiments have produced
chains of amino acids whose catalytic
activity is trivial at best. Bradley
and Thaxton (CH) Page 188

The
work the simulations are capable of accomplishing
is nothing like that within cells.

In
sum total the calculations and approaches to
solving the questions posed by thermodynamics
come down to the scientists statement:

...
we conclude that energy flow through
the system is capable of joining molecular
building blocks but appears to be incapable
of joining them in the very specific
ways necessary to have biological function. Bradley
and Thaxton (CH) Page 188

Added
Perspective:

We
may err on the side of presenting numerous examples
of what could not have happened. But that's where
we find ourselves, because no one is able to provide
the explanation of how it could have happened.
We looked previously at fine-tuned conditions
required to make the universe and our solar system—the
earth too—favorable to supporting life. Yet
the energy necessary to set the physical stage
of life was there from the beginning. The physics
and physical chemistry that stem from the big
bang is easily comprehended by comparison to the
biophysics and biochemistry that is built into
the puzzle of assembling life. Formation of stars
by condensing gases in outer space if favorable,
building biomolecules of just the right kind and
necessary concentration, along with assembly into
functioning life systems is not a thermodynamically
favorable proposition.

The
perspective we glean here is that life is quite
unique. Energy requirements for the chemistry
of life raise the bar once more. Explanations
go wanting. The most knowledgeable of the world's
scientists are still thinking about possibilities,
but without resolution or clear results. And science's
knowledge base has never been greater than today.

Again, we are adding
perspective to perspective—looking at all the angles. Here, we have
one more element of the WindowView that along with other perspectives guides
us to a conclusion that is very different from simply natural, material,
and evolutionary scenarios. If this were the only complication we might
just excuse it for a time. But if not excused out of hand, there is good
reason to see that life did not arise by simple chemicals or by self assembly—not
of its own accord and not simply by chance reactions over eons of time.
In fact, life appeared too quickly on the primitive earth to give eons of
time as an option.

Quotations
from "The Creation Hypothesis" (CH)
edited by J. P. Moreland are used by permission
of InterVarsity Press, P.O. Box 1400, Downers
Grove, IL 60515. www.ivpress.com All rights
reserved. No portion of this material may be
used without permission from InterVarsity Press.

Quotations
from "Not By Chance" (NBC) written
by L. Spetner, are used by permission granted
by Dr. Lee Spetner.

The WindowView drops many of the typical presumptions to take another look. What does scientific data tell us if we start without assumptions? And ... how contiguous is science information if examined along with scriptural perspectives provided by the Bible? The Bible is the only religious or holy book we know of that is in fact consistent with science. While not a textbook, the Scriptures are either contradictory or complementary to scientific perspectives. Have you looked at these perspectives? To see 'Science and Scripture in Harmony' is to reveal life, reality, and your future.

Writer / Editor: Dr. T. Peterson,
Director, WindowView.org

(040408)

For a general listing of books, visit the WindowView Book Page for: Science and Scripture .

References of Interest

Step Up To Life

Time spent looking ... through a window on life and choice ... brings the opportunity to see in a new light. The offer for you to Step Up To Life is presented on many of the web pages at WindowView. Without further explanation we offer you the steps here ... knowing that depending on what you have seen or may yet explore in the window ... these steps will be the most important of your life ...